Peel the shallots and slice them in half lengthwise. If your shallots are really small you can leave them whole.
Add the peeled and halved shallots to the bottom of a 9x13 baking dish or Dutch oven pot along with the extra virgin olive oil. Season with kosher salt and freshly cracked black pepper. Toss to combine, then spread them back out into a somewhat even layer and nestle in a few thyme sprigs.
Bake uncovered for 1 hour 20 minutes until the shallots are soft and tender.
Allow the shallot confit to cool to room temperature. Discard herb sprigs and then transfer it to an airtight container or jar. Pour over the olive oil from the pan. Make sure to submerge the shallots in the cooking oil completely. Top with a tightly sealed lid.
Store in the fridge for 1 month or the freezer for up to 3 months.
Notes
Make It Your Way: Substitutions & Variations
No fresh thyme? - you can use other fresh herbs such as rosemary, oregano, or sage. If you don't have any fresh herbs, you can also use bay leaves. Add-ins - red pepper flakes, lemon zest, a splash of red wine vinegar or white wine, or a pinch of cane sugar to bring out more sweetness in the shallots.
Variations
Shallot and garlic confit - add fresh garlic cloves.Mixed allium confit - add in any other vegetables in the allium plant family such as leeks, garlic, onions, scallions/green onions, or garlic scapes.